LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8553249 2.8553249 2.8553249 Created orthogonal box = (0.0000000 -46.040731 0.0000000) to (23.020365 46.040731 2.8553249) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.1874352 3.1874352 2.8553249 Created 260 atoms using lattice units in orthogonal box = (0.0000000 -46.040731 0.0000000) to (23.020365 46.040731 2.8553249) create_atoms CPU = 0.001 seconds 260 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.1874352 3.1874352 2.8553249 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -46.040731 0.0000000) to (23.020365 46.040731 2.8553249) create_atoms CPU = 0.001 seconds 261 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 26 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 521 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_807997826449_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.500 | 4.500 | 4.500 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1960.2143 0 -1960.2143 101150.72 69 0 -2140.5533 0 -2140.5533 7191.1616 Loop time of 1.25322 on 1 procs for 69 steps with 521 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1960.21433028585 -2140.55161492404 -2140.55331690765 Force two-norm initial, final = 532.19040 0.12584029 Force max component initial, final = 153.65915 0.023399458 Final line search alpha, max atom move = 1.0000000 0.023399458 Iterations, force evaluations = 69 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2136 | 1.2136 | 1.2136 | 0.0 | 96.84 Neigh | 0.010286 | 0.010286 | 0.010286 | 0.0 | 0.82 Comm | 0.017524 | 0.017524 | 0.017524 | 0.0 | 1.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01185 | | | 0.95 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5696.00 ave 5696 max 5696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71440.0 ave 71440 max 71440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71440 Ave neighs/atom = 137.12092 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.504 | 4.504 | 4.504 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -2140.5533 0 -2140.5533 7191.1616 6052.5717 75 0 -2140.6537 0 -2140.6537 0.1990058 6078.0363 Loop time of 0.0886809 on 1 procs for 6 steps with 521 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2140.55331690763 -2140.65214702102 -2140.65368847746 Force two-norm initial, final = 50.380608 0.22152747 Force max component initial, final = 40.961848 0.082061561 Final line search alpha, max atom move = 0.00019374516 1.5899030e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.084273 | 0.084273 | 0.084273 | 0.0 | 95.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010691 | 0.0010691 | 0.0010691 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003339 | | | 3.77 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5888.00 ave 5888 max 5888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71356.0 ave 71356 max 71356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71356 Ave neighs/atom = 136.95969 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.642 | 4.642 | 4.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2140.6537 0 -2140.6537 0.1990058 Loop time of 6.124e-06 on 1 procs for 0 steps with 521 atoms 196.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.124e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5888.00 ave 5888 max 5888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71284.0 ave 71284 max 71284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71284 Ave neighs/atom = 136.82150 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.642 | 4.642 | 4.642 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -2140.6537 -2140.6537 22.985468 92.55209 2.8570886 0.1990058 0.1990058 17.443519 4.7983706 -21.644872 2.3144851 117.30523 Loop time of 7.527e-06 on 1 procs for 0 steps with 521 atoms 212.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.527e-06 | | |100.00 Nlocal: 521.000 ave 521 max 521 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5888.00 ave 5888 max 5888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35642.0 ave 35642 max 35642 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71284.0 ave 71284 max 71284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71284 Ave neighs/atom = 136.82150 Neighbor list builds = 0 Dangerous builds = 0 521 -2140.65368847746 eV 2.31448507266767 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01